Our understanding of the functional role of posttranscriptionally modified nucleosides in protein synthesis, especially those localized to ribosomal ribonucleic acids (rRNAs), is limited largely by the lack of methods that can identify and characterize their interactions with proteins. The long-term goal of our research has been and continues to be to develop appropriate mass spectrometric approaches to characterize the structure of the ribosome in terms of RNA and RNA-protein interactions. The goals of this renewal are to develop new and improved mass spectrometry (MS) approaches to identify and characterize RNA-protein interactions within the ribosome, and to apply these methods to obtain biologically relevant information about ribosome structure and function. The first aim will focus on cross-link identification and sequencing. Those developments will be used to identify specific recognition elements of the RNAs and ribosomal proteins involved in the initiation step in protein synthesis. The second aim will focus on identifying and quantifying pseudouridine. Those developments will be used to quantitatively characterize pseudouridines present in 23S rRNA. The significance of these proposed studies include bioanalytical MS developments for identifying and sequencing RNA-protein (or DNA-protein) cross-links and the quantitative determination of pseudouridine with site specificity. This research plan will yield important biological information on the ribosome including how messages lacking the Shine-Dalgarno motif are bound before translation, the role of ribosomal protein L31 in the initiation step, and the mode of action for the 23S rRNA pseudouridine synthase RluD. Innovations in the proposed research plan include developing liquid chromatography inductively coupled plasma mass spectrometry (LC-ICP-MS) for selective identification of nucleic acid-protein cross-links, the use of electron transfer dissocation (ETD) for sequencing the peptide moiety in an oligonucleotide:peptide heteroconjugate, which leads to a robust MS/MS method for cross-link sequencing, and creating a quantitative assay for pseudouridine. This research plan will yield new and improved approaches for characterizing RNA-protein interactions. Additionally, while the technology and method developments from this research will be used to characterize the ribosome, many of the developments will have broad applicability for investigators interested in characterizing other ribonucleoprotein complexes, DNA-protein complexes, or other nucleic acid systems. Importantly, this research plan will provide new tools and information of importance about protein synthesis, which is fundamentally significant and relevant to human health.